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Crystal Structure of the Listeria monocytogenes CadC in complex with DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9T6R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.005M Sodium chromate tetrahydrate, 0.005M Sodium molybdate dihydrate, 0.005M Sodium tungstate dihydrate,
0.005M Sodium orthovanadate,
0.1M BES pH 7.5, 0.1M Triethanolamine (TEA) pH 7.5, 15% w/v PEG 3000, 20% v/v 1, 2, 4-Butanetriol, 1% w/v NDSB 256
Crystal Properties Matthews coefficient Solvent content 2.1 47.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.503 α = 90 b = 82.073 β = 98.306 c = 38.476 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 4M 2025-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.9677 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.69 42.7 97.47 0.05328 0.06837 0.04227 0.998 4.82 2.4 33727 29.19
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.69 1.74 1.648 2.115 1.309 0.408 0.48
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.69 42.68 1.34 33722 1641 97.45 0.2496 0.2478 0.2509 0.2854 0.2877 40.37
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 23.1723 f_angle_d 0.8645 f_chiral_restr 0.0454 f_bond_d 0.007 f_plane_restr 0.0051
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1598 Nucleic Acid Atoms 814 Solvent Atoms 145 Heterogen Atoms 4
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing